Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds

Metabolic Engineering

Volumn 35, Issue , 2016, Pages 46-54

  Martínez, Igor ^a   Mohamed, Magdy El Said ^b   Rozas, Daniel ^a   García, José Luis ^a   Díaz, Eduardo ^a  

^a CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^b SAUDI ARAMCO   (Saudi Arabia)

Author keywords

2 hydroxybiphenyll dsz cassettes; Dibenzothiophene; Pseudomonas putida; Synthetic bacterial consortia

Indexed keywords

BACTERIA; ENZYME INHIBITION; ENZYMES; REACTION INTERMEDIATES; SULFUR; SULFUR COMPOUNDS;

2-HYDROXYBIPHENYL; 2-HYDROXYBIPHENYLL DSZ CASSETTES; BACTERIAL CONSORTIUM; DIBENZOTHIOPHENES; FUNCTIONAL UNITS; PSEUDOMONAS PUTIDA; RATIONAL DESIGN; REVALORIZATION;

METABOLIC ENGINEERING;

2 HYDROXYBIPHENYL; 2 HYDROXYBIPHENYLSULFINATE; DIBENZOTHIOPHENE DERIVATIVE; OIL; OIL SULFUR COMPOUND; OXYGENASE INHIBITOR; SULFUR DERIVATIVE; UNCLASSIFIED DRUG; UNSPECIFIC MONOOXYGENASE;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; BIOCATALYST; BIOTRANSFORMATION; CHEMICAL MODIFICATION; DESULFURIZATION; DSZA GENE; DSZB GENE; DSZC GENE; DSZD GENE; GENE CASSETTE; GENETIC RECOMBINATION; METABOLIC ENGINEERING; MONOCULTURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PSEUDOMONAS PUTIDA; REVALORIZATION; ENZYMOLOGY; GENETICS; METABOLISM; MICROBIAL CONSORTIUM;

METABOLIC ENGINEERING; MICROBIAL CONSORTIA; PSEUDOMONAS PUTIDA; SULFUR COMPOUNDS;

EID: 84957799019     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2016.01.005     Document Type: Article

References (55)

1. Abin-Fuentes A., Mohamed Mel S., Wang D.I., Prather K.L. Exploring the mechanism of biocatalyst inhibition in microbial desulfurization. Appl. Environ. Microbiol. 2013, 79:7807-7817.
2. Aggarwal S., Karimi I.A., Kilbane J.J., Lee D.Y. Roles of sulfite oxidoreductase and sulfite reductase in improving desulfurization by Rhodococcus erythropolis. Mol. Biosyst. 2012, 8:2724-2732.
3. Alves L., Paixao S.M. Fructophilic behaviour of Gordonia alkanivorans strain 1B during dibenzothiophene desulfurization process. New Biotechnol. 2014, 31:73-79.
4. Babich I.V., Moulijn J.A. Science and technology of novel processes for deep desulfurization of oil refinery streams: a review. Fuel 2003, 82:607-631.
5. Bacchus W., Fussenegger M. Engineering of synthetic intercellular communication systems. Metab. Eng. 2013, 16:33-41.
6. Boniek D., Figueiredo D., dos Santos A., de Resende Stoianoff M. Biodesulfurization: a mini review about the immediate search for the future technology. Clean Technol. Environ. Policy 2015, 17:29-37.
7. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72:248-254.
8. Campos-Martín J.M., Capel-Sánchez M.C., Fierro J.L.G. Highly efficient deep desulfurization of fuels by chemical oxidation. Green Chem. 2004, 6:557-562.
9. Coco W.M., Levinson W.E., Crist M.J., Hektor H.J., Darzins A., Pienkos P.T., Squires C.H., Monticello D.J. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat. Biotechnol. 2001, 19:354-359.
10. Davoodi-Dehaghani F., Vosoughi M., Ziaee A.A. Biodesulfurization of dibenzothiophene by a newly isolated Rhodococcus erythropolis strain. Bioresour. Technol. 2010, 101:1102-1105.
11. del Olmo C.H., Alcón A., Santos V.E., García-Ochoa F. Modeling the production of a Rhodococcus erythropolis IGTS8 biocatalyst for DBT biodesulfurization: Influence of media composition. Enzym. Microb. Technol. 2005, 37:157-166.
12. Díaz E., García J.L. Genetics engineering for removal of sulfur and nitrogen from fuel heterocycles. Handbook of Hydrocarbon and Lipid Microbiology. 2010, 2787-2801. Springer, Berlin Heidelberg, Berlin. K.N. Timmis (Ed.).
13. Du J., Bai W., Song H., Yuan Y.J. Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-l-gulonic acid production in Ketogulonigenium vulgare-Bacillus cereus consortium. Metab. Eng. 2013, 19:50-56.
14. Duarte G.F., Rosado A.S., Seldin L., de Araujo W., van Elsas J.D. Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes. Appl. Environ. Microbiol. 2001, 67:1052-1062.
15. Franklin F.C., Bagdasarian M., Bagdasarian M.M., Timmis K.N. Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc. Natl. Acad. Sci. USA 1981, 78:7458-7462.
16. Galán B., Díaz E., García J.L. Enhancing desulphurization by engineering a flavin reductase-encoding gene cassette in recombinant biocatalysts. Environ. Microbiol. 2000, 2:687-694.
17. Galán B., Díaz E., Prieto M.A., García J.L. Functional analysis of the small component of the 4-hydroxyphenylacetate 3-monooxygenase of Escherichia coli W: a prototype of a new Flavin:NAD(P)H reductase subfamily. J. Bacteriol. 2000, 182:627-636.
18. Gallagher J.R., Olson E.S., Stanley D.C. Microbial desulfurization of dibenzothiophene: a sulfur-specific pathway. FEMS Microbiol. Lett. 1993, 107:31-35.
19. Gallardo M.E., Ferrandez A., De Lorenzo V., García J.L., Diaz E. Designing recombinant Pseudomonas strains to enhance biodesulfurization. J. Bacteriol. 1997, 179:7156-7160.
20. Gray K.A., Mrachko G.T., Squires C.H. Biodesulfurization of fossil fuels. Curr. Opin. Microbiol. 2003, 6:229-235.
21. Gray K.A., Pogrebinsky O.S., Mrachko G.T., Xi L., Monticello D.J., Squires C.H. Molecular mechanisms of biocatalytic desulfurization of fossil fuels. Nat. Biotechnol. 1996, 14:1705-1709.
22. Gupta N., Roychoudhury P.K., Deb J.K. Biotechnology of desulfurization of diesel: prospects and challenges. Appl. Microbiol. Biotechnol. 2005, 66:356-366.
23. Hanson G., Kemp D.S. Convenient routes to 4,4″-functionalized o-terphenyls and 2,2'-functionalized biphenyls. J. Org. Chem. 1981, 46:5441-5443.
24. Kalyuzhnaya M.G., Puri A.W., Lidstrom M.E. Metabolic engineering in methanotrophic bacteria. Metab. Eng. 2015, 29:142-152.
25. Kamali N., Tavallaie M., Bambai B., Karkhane A., Miri M. Site-directed mutagenesis enhances the activity of NADH-FMN oxidoreductase (DszD) activity of Rhodococcus erythropolis. Biotechnol. Lett. 2010, 32:921-927.
26. Kilbane J.J. Microbial biocatalyst developments to upgrade fossil fuels. Curr. Opin. Biotechnol. 2006, 17:305-314.
27. Kilbane J.J., Jackowski K. Biodesulfurization of water-soluble coal-derived material by Rhodococcus rhodochrous IGTS8. Biotechnol. Bioeng. 1992, 40:1107-1114.
28. Li G.Q., Li S.S., Zhang M.L., Wang J., Zhu L., Liang F.L., Liu R.L., Ma T. Genetic rearrangement strategy for optimizing the dibenzothiophene biodesulfurization pathway in Rhodococcus erythropolis. Appl. Environ. Microbiol. 2008, 74:971-976.
29. Li M.Z., Squires C.H., Monticello D.J., Childs J.D. Genetic analysis of the dsz promoter and associated regulatory regions of Rhodococcus erythropolis IGTS8. J. Bacteriol. 1996, 178:6409-6418.
30. Ma T., Li G., Li J., Liang F., Liu R. Desulfurization of dibenzothiophene by Bacillus subtilis recombinants carrying dszABC and dszD genes. Biotechnol. Lett. 2006, 28:1095-1100.
31. Martín A.B., Alcón A., Santos V.E., García-Ochoa F. Production of a Biocatalyst of Pseudomonas putida CECT5279 for dibenzothiophene (DBT) biodesulfurization for different media compositions. Energy Fuels 2004, 18:851-857.
32. Martín A.B., Alcón A., Santos V.E., García-Ochoa F. Production of a biocatalyst of Pseudomonas putida CECT5279 for DBT biodesulfurization: Influence of the operational conditions. Energy Fuels 2005, 19:775-782.
33. Mohebali G., Ball A.S. Biocatalytic desulfurization (BDS) of petrodiesel fuels. Microbiology 2008, 154:2169-2183.
34. Monticello D.J. Biodesulfurization and the upgrading of petroleum distillates. Curr. Opin. Biotechnol. 2000, 11:540-546.
35. Moreno-Ruiz E., Hernáez M.J., Martínez-Pérez O., Santero E. Identification and functional characterization of Sphingomonas macrogolitabida strain TFA genes involved in the first two steps of the tetralin catabolic pathway. J. Bacteriol. 2003, 185:2026-2030.
36. Nikel P.I., Martínez-García E., de Lorenzo V. Biotechnological domestication of pseudomonads using synthetic biology. Nat. Rev. Microbiol. 2014, 12:368-379.
37. Nuhu A. Bio-catalytic desulfurization of fossil fuels: a mini review. Rev. Environ. Sci. Biotechnol. 2013, 12:9-23.
38. Ohshiro T., Ohkita R., Takikawa T., Manabe M., Lee W.C., Tanokura M., Izumi Y. Improvement of 2'-Hydroxybiphenyl-2-sulfinate desulfinase, an enzyme involved in the dibenzothiophene desulfurization pathway, from Rhodococcus erythropolis KA2-5-1 by site-directed mutagenesis. Biosci. Biotechnol. Biochem. 2007, 71:2815-2821.
39. Oldfield C., Pogrebinsky O., Simmonds J., Olson E.S., Kulpa C.F. Elucidation of the metabolic pathway for dibenzothiophene desulphurization by Rhodococcus sp. strain IGTS8 (ATCC 53968). Microbiology 1997, 143(Pt 9):2961-2973.
40. Ortiz-Marquez J.C.F., Do Nascimento M., Curatti L. Metabolic engineering of ammonium release for nitrogen-fixing multispecies microbial cell-factories. Metab. Eng. 2014, 23:154-164.
41. Parales R.E., Ju K.-S., Rollefson J.B., Ditty J. Bioavailability, chemotaxis, and transport of organic pollutants. Microbial Biodegradation: Genomics and Molecular Biology 2008, 145-187. Caister Academic Press, Norfolk, United Kingdom. E. Díaz (Ed.).
42. Piddington C.S., Kovacevich B.R., Rambosek J. Sequence and molecular characterization of a DNA region encoding the dibenzothiophene desulfurization operon of Rhodococcus sp. strain IGTS8. Appl. Environ. Microbiol. 1995, 61:468-475.
43. Prieto M.A., Díaz E., García J.L. Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: engineering a mobile aromatic degradative cluster. J. Bacteriol. 1996, 178:111-120.
44. Rashtchi M., Mohebali G.H., Akbarnejad M.M., Towfighi J., Rasekh B., Keytash A. Analysis of biodesulfurization of model oil system by the bacterium, strain RIPI-22. Biochem. Eng. J. 2006, 29:169-173.
45. Reichmuth D.S., Hittle J.L., Blanch H.W., Keasling J.D. Biodesulfurization of dibenzothiophene in Escherichia coli is enhanced by expression of a Vibrio harveyi oxidoreductase gene. Biotechnol. Bioeng. 2000, 67:72-79.
46. Sambrook J., Russell D.W. Molecular Cloning: a Laboratory Manual 2001, Cold Spring Harbor Laboratory Press. Cold Spring Harbor, New York.
47. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 1977, 74:5463-5467.
48. Sauer M., Mattanovich D. Construction of microbial cell factories for industrial bioprocesses. J. Chem. Technol. Biotechnol. 2012, 87:445-450.
49. Shavandi M., Sadeghizadeh M., Zomorodipour A., Khajeh K. Biodesulfurization of dibenzothiophene by recombinant Gordonia alkanivorans RIPI90A. Bioresour. Technol. 2009, 100:475-479.
50. Soleimani M., Bassi A., Margaritis A. Biodesulfurization of refractory organic sulfur compounds in fossil fuels. Biotechnol. Adv. 2007, 25:570-596.
51. Stanislaus A., Marafi A., Rana M.S. Recent advances in the science and technology of ultra low sulfur diesel (ULSD) production. Catal. Today 2010, 153:1-68.
52. Tao F., Zhao P., Li Q., Su F., Yu B., Ma C., Tang H., Tai C., Wu G., Xu P. Genome sequence of Rhodococcus erythropolis XP, a biodesulfurizing bacterium with industrial potential. J. Bacteriol. 2011, 193:6422-6423.
53. Wang Z.-l, Wang D., Li Q., Li W.-L., Tang H., Xing J.-M. Enhanced biodesulfurization by expression of dibenzothiophene uptake genes in Rhodococcus erythropolis. World J. Microbiol. Biotechnol. 2011, 27:1965-1970.
54. Xu P., Feng J., Yu B., Li F., Ma C. Recent developments in biodesulfurization of fossil fuels. Adv. Biochem. Eng. Biotechnol. 2009, 113:255-274.
55. Zargar A., Quan D.N., Emamian M., Tsao C.Y., Wu H.-C., Virgile C.R., Bentley W.E. Rational design of 'controller cells' to manipulate protein and phenotype expression. Metab. Eng. 2015, 30:61-68.